Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene

Abstract

BackgroundSmall hydrophobic (SH) gene is one of the mostly diverse genomic regions of human respiratory syncytial virus (HRSV). Its coding region constitutes less than 50% of the complete gene length, enabling SH gene to be highly variable and the SH protein highly conserved. In standard HRSV molecular epidemiology studies, solely sequences of the second hypervariable region of the glycoprotein gene (HVR2) are analyzed. To what extent do the strains identical in HVR2 differ elsewhere in genomes is rarely investigated. Our goal was to investigate whether diversity and inter-genotype differences observed for HVR2 are also present in the SH gene.MethodsWe sequenced 198 clinical samples collected within a limited area and time frame. In this HRSV collection, rapid and significant changes in HVR2 occurred.ResultsOver 20% of strains from this pool (containing HRSV genotypes NA1, ON1, GA5, BA9 and BA10) would be incorrectly assumed to be identical to another strain if only the HVR2 region was analysed. The majority of differences found in SH gene were located in the 5′ untranslated region (UTR). Seven indels were detected, one was genotype GA5 specific. An in-frame deletion of 9 nucleotides (coding for amino acids 49–51) was observed in one of group A strains. Fifteen different SH protein sequences were detected; 68% of strains possessed the consensus sequence and most of others differed from the consensus in only one amino acid (only 4 strains differed in 2 amino acids). The majority of differing amino acids in group A viruses had the same identity as the corresponding amino acids in group B strains. When analysis was restricted to strains with identical HVR2 nucleotide sequences and differing SH protein sequences, 75% of differences observed in the SH ectodomain were located within region coding for amino acids 49–51.ConclusionsBasing HRSV molecular epidemiology studies solely on HVR2 largely underestimates the complexity of circulating virus populations. In strain identification, broadening of the genomic target sequence to SH gene would provide a more comprehensive insight into viral pool versatility and its evolutionary processes.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1020-9) contains supplementary material, which is available to authorized users.

Circulation patterns and molecular epidemiology of human respiratory syncytial virus over five consecutive seasons in Morocco

“…Among all relevant HRSV genes, the attachment glycoprotein gene holds the highest number of variations that can affect viral infection and transmission 17 . Currently, genotyping of HRSV strains is based on the second hypervariable region of gene G (HVR‐2) 5,10 . The phylogenetic analysis based on the alignment of HRSV G sequences, included sequences of HRSV‐A and HRSV‐B strains circulating in Morocco along with representative strains of known genotypes retrieved from the Genbank 18 as at February 16, 2023.…”

“… 17 Currently, genotyping of HRSV strains is based on the second hypervariable region of gene G (HVR‐2). 5 , 10 The phylogenetic analysis based on the alignment of HRSV G sequences, included sequences of HRSV‐A and HRSV‐B strains circulating in Morocco along with representative strains of known genotypes retrieved from the Genbank 18 as at February 16, 2023. Identical sequences were detected and removed using “ElimDupes Duplicate Sequence Removal tool.” 19 Multiple sequence alignments of the HVR‐2 of gene G compared to available reference genotypes were performed using the ClustalW algorithm.…”

“…HRSV is divided into two antigenic subtypes (A and B) that are mostly distinguished by differences in the viral attachment (G) protein and each has been divided into multiple genotypes 4 . The sequence of the G gene is the most variable; thus, all molecular epidemiology studies of HRSV have focused on the second hypervariable region in the C‐terminal (HVR2) of the G protein and it has been used for virus genotyping 5 . Fifteen genotypes of HRSV‐A (GA1 to −7, SAA1, CB‐A, NA1 to −4, ON1 and ON2) and 29 genotypes of HRSV‐B (BA1 to −14, GB1 to −5, SAB1 to −4, URU1, URU2, CB1, BA‐C, CB‐B, and THB) have been described 6–10 .…”

“… 4 The sequence of the G gene is the most variable; thus, all molecular epidemiology studies of HRSV have focused on the second hypervariable region in the C‐terminal (HVR2) of the G protein and it has been used for virus genotyping. 5 Fifteen genotypes of HRSV‐A (GA1 to −7, SAA1, CB‐A, NA1 to −4, ON1 and ON2) and 29 genotypes of HRSV‐B (BA1 to −14, GB1 to −5, SAB1 to −4, URU1, URU2, CB1, BA‐C, CB‐B, and THB) have been described. 6 , 7 , 8 , 9 , 10 Among these genotypes, HRSV‐A ON1 and HRSV‐B BA with respectively 72 and 60 nucleotide duplications within the second hypervariable region of the G gene spread rapidly throughout the world and have been detected globally.…”

Clinical and biological consequences of respiratory syncytial virus genetic diversity

“…Both RSV-A and RSV-B have high nucleotide diversity in the 5′UTR of SH, potentially signaling selection for SH expression that may influence RSV pathogenesis. 13 , 62 In a cohort of RSV+ infants in Vietnam, M2-2 was found to be under positive selection, with an increased ratio of nonsynonymous mutations to synonymous mutations in both RSV-A and RSV-B isolates. 63 Some mutational hotspots have also been found to be subtype specific, including sites in NS1 and N in RSV-A with still uncharacterized functionality.…”